Sidebar

IEU GWAS information

Trait: interleukin 27.

name	value
id	PROT-b-14
trait	interleukin 27
pmid	28369058
year	2018
author	Folkersen L
population	European
sex	Males and Females
sample_size	3394
build	HG19/GRCh37
group_name	public
access	public
nsnp	5270646
mr	1
category	Immune system
subcategory	Protein
batch	PROT-b

Report information

name	value
gwas_id	prot-b-14
bcf_file	prot-b-14.vcf.gz
qc_metrics_file	qc_metrics.json
metadata	metadata.json
refdata	1kg_v3_nomult.bcf
compile_time	2020-05-09 14:29 BST
build_version	run_igd-8f4f4c9-2020-05-09

Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

QQ plot

qq_plot

AF plot

af_plot

P-Z plot

pz_plot

beta_std plot

beta_std_plot

Metadata

{
    "fileformat": "VCFv4.2",
    "FILTER": "<ID=PASS,Description=\"All filters passed\">",
    "INFO": "<ID=AF,Number=A,Type=Float,Description=\"Allele Frequency\">",
    "FORMAT": "<ID=ES,Number=A,Type=Float,Description=\"Effect size estimate relative to the alternative allele\">",
    "FORMAT.1": "<ID=SE,Number=A,Type=Float,Description=\"Standard error of effect size estimate\">",
    "FORMAT.2": "<ID=LP,Number=A,Type=Float,Description=\"-log10 p-value for effect estimate\">",
    "FORMAT.3": "<ID=AF,Number=A,Type=Float,Description=\"Alternate allele frequency in the association study\">",
    "FORMAT.4": "<ID=SS,Number=A,Type=Float,Description=\"Sample size used to estimate genetic effect\">",
    "FORMAT.5": "<ID=EZ,Number=A,Type=Float,Description=\"Z-score provided if it was used to derive the EFFECT and SE fields\">",
    "FORMAT.6": "<ID=SI,Number=A,Type=Float,Description=\"Accuracy score of summary data imputation\">",
    "FORMAT.7": "<ID=NC,Number=A,Type=Float,Description=\"Number of cases used to estimate genetic effect\">",
    "FORMAT.8": "<ID=ID,Number=1,Type=String,Description=\"Study variant identifier\">",
    "META": "<ID=TotalVariants,Number=1,Type=Integer,Description=\"Total number of variants in input\">",
    "META.1": "<ID=VariantsNotRead,Number=1,Type=Integer,Description=\"Number of variants that could not be read\">",
    "META.2": "<ID=HarmonisedVariants,Number=1,Type=Integer,Description=\"Total number of harmonised variants\">",
    "META.3": "<ID=VariantsNotHarmonised,Number=1,Type=Integer,Description=\"Total number of variants that could not be harmonised\">",
    "META.4": "<ID=SwitchedAlleles,Number=1,Type=Integer,Description=\"Total number of variants strand switched\">",
    "META.5": "<ID=TotalControls,Number=1,Type=Integer,Description=\"Total number of controls in the association study\">",
    "META.6": "<ID=TotalCases,Number=1,Type=Integer,Description=\"Total number of cases in the association study\">",
    "META.7": "<ID=StudyType,Number=1,Type=String,Description=\"Type of GWAS study [Continuous or CaseControl]\">",
    "SAMPLE": "<ID=PROT-b-14,TotalVariants=5136688,VariantsNotRead=0,HarmonisedVariants=5135036,VariantsNotHarmonised=1652,SwitchedAlleles=3978052,TotalControls=3394.0,StudyType=Continuous>",
    "contig": "<ID=1,length=249250621,assembly=HG19/GRCh37>",
    "contig.1": "<ID=2,length=243199373,assembly=HG19/GRCh37>",
    "contig.2": "<ID=3,length=198022430,assembly=HG19/GRCh37>",
    "contig.3": "<ID=4,length=191154276,assembly=HG19/GRCh37>",
    "contig.4": "<ID=5,length=180915260,assembly=HG19/GRCh37>",
    "contig.5": "<ID=6,length=171115067,assembly=HG19/GRCh37>",
    "contig.6": "<ID=7,length=159138663,assembly=HG19/GRCh37>",
    "contig.7": "<ID=8,length=146364022,assembly=HG19/GRCh37>",
    "contig.8": "<ID=9,length=141213431,assembly=HG19/GRCh37>",
    "contig.9": "<ID=10,length=135534747,assembly=HG19/GRCh37>",
    "contig.10": "<ID=11,length=135006516,assembly=HG19/GRCh37>",
    "contig.11": "<ID=12,length=133851895,assembly=HG19/GRCh37>",
    "contig.12": "<ID=13,length=115169878,assembly=HG19/GRCh37>",
    "contig.13": "<ID=14,length=107349540,assembly=HG19/GRCh37>",
    "contig.14": "<ID=15,length=102531392,assembly=HG19/GRCh37>",
    "contig.15": "<ID=16,length=90354753,assembly=HG19/GRCh37>",
    "contig.16": "<ID=17,length=81195210,assembly=HG19/GRCh37>",
    "contig.17": "<ID=18,length=78077248,assembly=HG19/GRCh37>",
    "contig.18": "<ID=19,length=59128983,assembly=HG19/GRCh37>",
    "contig.19": "<ID=20,length=63025520,assembly=HG19/GRCh37>",
    "contig.20": "<ID=21,length=48129895,assembly=HG19/GRCh37>",
    "contig.21": "<ID=22,length=51304566,assembly=HG19/GRCh37>",
    "contig.22": "<ID=X,length=155270560,assembly=HG19/GRCh37>",
    "contig.23": "<ID=Y,length=59373566,assembly=HG19/GRCh37>",
    "contig.24": "<ID=MT,length=16569,assembly=HG19/GRCh37>",
    "contig.25": "<ID=GL000207.1,length=4262,assembly=HG19/GRCh37>",
    "contig.26": "<ID=GL000226.1,length=15008,assembly=HG19/GRCh37>",
    "contig.27": "<ID=GL000229.1,length=19913,assembly=HG19/GRCh37>",
    "contig.28": "<ID=GL000231.1,length=27386,assembly=HG19/GRCh37>",
    "contig.29": "<ID=GL000210.1,length=27682,assembly=HG19/GRCh37>",
    "contig.30": "<ID=GL000239.1,length=33824,assembly=HG19/GRCh37>",
    "contig.31": "<ID=GL000235.1,length=34474,assembly=HG19/GRCh37>",
    "contig.32": "<ID=GL000201.1,length=36148,assembly=HG19/GRCh37>",
    "contig.33": "<ID=GL000247.1,length=36422,assembly=HG19/GRCh37>",
    "contig.34": "<ID=GL000245.1,length=36651,assembly=HG19/GRCh37>",
    "contig.35": "<ID=GL000197.1,length=37175,assembly=HG19/GRCh37>",
    "contig.36": "<ID=GL000203.1,length=37498,assembly=HG19/GRCh37>",
    "contig.37": "<ID=GL000246.1,length=38154,assembly=HG19/GRCh37>",
    "contig.38": "<ID=GL000249.1,length=38502,assembly=HG19/GRCh37>",
    "contig.39": "<ID=GL000196.1,length=38914,assembly=HG19/GRCh37>",
    "contig.40": "<ID=GL000248.1,length=39786,assembly=HG19/GRCh37>",
    "contig.41": "<ID=GL000244.1,length=39929,assembly=HG19/GRCh37>",
    "contig.42": "<ID=GL000238.1,length=39939,assembly=HG19/GRCh37>",
    "contig.43": "<ID=GL000202.1,length=40103,assembly=HG19/GRCh37>",
    "contig.44": "<ID=GL000234.1,length=40531,assembly=HG19/GRCh37>",
    "contig.45": "<ID=GL000232.1,length=40652,assembly=HG19/GRCh37>",
    "contig.46": "<ID=GL000206.1,length=41001,assembly=HG19/GRCh37>",
    "contig.47": "<ID=GL000240.1,length=41933,assembly=HG19/GRCh37>",
    "contig.48": "<ID=GL000236.1,length=41934,assembly=HG19/GRCh37>",
    "contig.49": "<ID=GL000241.1,length=42152,assembly=HG19/GRCh37>",
    "contig.50": "<ID=GL000243.1,length=43341,assembly=HG19/GRCh37>",
    "contig.51": "<ID=GL000242.1,length=43523,assembly=HG19/GRCh37>",
    "contig.52": "<ID=GL000230.1,length=43691,assembly=HG19/GRCh37>",
    "contig.53": "<ID=GL000237.1,length=45867,assembly=HG19/GRCh37>",
    "contig.54": "<ID=GL000233.1,length=45941,assembly=HG19/GRCh37>",
    "contig.55": "<ID=GL000204.1,length=81310,assembly=HG19/GRCh37>",
    "contig.56": "<ID=GL000198.1,length=90085,assembly=HG19/GRCh37>",
    "contig.57": "<ID=GL000208.1,length=92689,assembly=HG19/GRCh37>",
    "contig.58": "<ID=GL000191.1,length=106433,assembly=HG19/GRCh37>",
    "contig.59": "<ID=GL000227.1,length=128374,assembly=HG19/GRCh37>",
    "contig.60": "<ID=GL000228.1,length=129120,assembly=HG19/GRCh37>",
    "contig.61": "<ID=GL000214.1,length=137718,assembly=HG19/GRCh37>",
    "contig.62": "<ID=GL000221.1,length=155397,assembly=HG19/GRCh37>",
    "contig.63": "<ID=GL000209.1,length=159169,assembly=HG19/GRCh37>",
    "contig.64": "<ID=GL000218.1,length=161147,assembly=HG19/GRCh37>",
    "contig.65": "<ID=GL000220.1,length=161802,assembly=HG19/GRCh37>",
    "contig.66": "<ID=GL000213.1,length=164239,assembly=HG19/GRCh37>",
    "contig.67": "<ID=GL000211.1,length=166566,assembly=HG19/GRCh37>",
    "contig.68": "<ID=GL000199.1,length=169874,assembly=HG19/GRCh37>",
    "contig.69": "<ID=GL000217.1,length=172149,assembly=HG19/GRCh37>",
    "contig.70": "<ID=GL000216.1,length=172294,assembly=HG19/GRCh37>",
    "contig.71": "<ID=GL000215.1,length=172545,assembly=HG19/GRCh37>",
    "contig.72": "<ID=GL000205.1,length=174588,assembly=HG19/GRCh37>",
    "contig.73": "<ID=GL000219.1,length=179198,assembly=HG19/GRCh37>",
    "contig.74": "<ID=GL000224.1,length=179693,assembly=HG19/GRCh37>",
    "contig.75": "<ID=GL000223.1,length=180455,assembly=HG19/GRCh37>",
    "contig.76": "<ID=GL000195.1,length=182896,assembly=HG19/GRCh37>",
    "contig.77": "<ID=GL000212.1,length=186858,assembly=HG19/GRCh37>",
    "contig.78": "<ID=GL000222.1,length=186861,assembly=HG19/GRCh37>",
    "contig.79": "<ID=GL000200.1,length=187035,assembly=HG19/GRCh37>",
    "contig.80": "<ID=GL000193.1,length=189789,assembly=HG19/GRCh37>",
    "contig.81": "<ID=GL000194.1,length=191469,assembly=HG19/GRCh37>",
    "contig.82": "<ID=GL000225.1,length=211173,assembly=HG19/GRCh37>",
    "contig.83": "<ID=GL000192.1,length=547496,assembly=HG19/GRCh37>",
    "gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/folkersen/processed/PROT-b-14/PROT-b-14_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2019-10-28T01:57:07.086911",
    "bcftools_annotateVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
    "bcftools_annotateCommand": "annotate -a /mnt/storage/home/gh13047/mr-eve/vcf-reference-datasets/dbsnp/dbsnp.v153.b37.vcf.gz -c ID -o /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/folkersen/processed/PROT-b-14/PROT-b-14.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/folkersen/processed/PROT-b-14/PROT-b-14_data.vcf.gz; Date=Mon Oct 28 02:42:47 2019",
    "bcftools_viewVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
    "bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/prot-b-14/prot-b-14.vcf.gz; Date=Sat May  9 14:20:46 2020"
}

LDSC

*********************************************************************
* LD Score Regression (LDSC)
* Version 1.0.1
* (C) 2014-2019 Brendan Bulik-Sullivan and Hilary Finucane
* Broad Institute of MIT and Harvard / MIT Department of Mathematics
* GNU General Public License v3
*********************************************************************
Call: 
./ldsc.py \
--h2 /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/folkersen-pqtl-gwas-import/processed/PROT-b-14/PROT-b-14.vcf.gz \
--ref-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/folkersen-pqtl-gwas-import/processed/PROT-b-14/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Mon Oct 28 22:10:18 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/folkersen-pqtl-gwas-import/processed/PROT-b-14/PROT-b-14.vcf.gz ...
Read summary statistics for 5135036 SNPs.
Dropped 1 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/[1-22] ...
Read reference panel LD Scores for 1290028 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 759193 SNPs remain.
After merging with regression SNP LD, 759193 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.1053 (0.1797)
Lambda GC: 0.9936
Mean Chi^2: 0.9975
Intercept: 1.0056 (0.0098)
Ratio: NA (mean chi^2 < 1)
Analysis finished at Mon Oct 28 22:11:08 2019
Total time elapsed: 49.52s

QC metrics

Metrics

{
    "af_correlation": 0.9563,
    "inflation_factor": 0.9916,
    "mean_EFFECT": 0.0058,
    "n": "-Inf",
    "n_snps": 5135036,
    "n_clumped_hits": 2,
    "n_p_sig": 133,
    "n_mono": 545,
    "n_ns": 317497,
    "n_mac": 0,
    "is_snpid_unique": false,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 377170,
    "n_est": "NA",
    "ratio_se_n": "NA",
    "mean_diff": "NaN",
    "ratio_diff": "NaN",
    "sd_y_est1": "NaN",
    "sd_y_est2": "NA",
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 759193,
    "ldsc_nsnp_merge_regression_ld": 759193,
    "ldsc_observed_scale_h2_beta": "NA",
    "ldsc_observed_scale_h2_se": "NA",
    "ldsc_intercept_beta": 1.0056,
    "ldsc_intercept_se": 0.0098,
    "ldsc_lambda_gc": 0.9936,
    "ldsc_mean_chisq": 0.9975,
    "ldsc_ratio": -2.24
}

Flags

name	value
af_correlation	FALSE
inflation_factor	FALSE
n	TRUE
is_snpid_non_unique	TRUE
mean_EFFECT_nonfinite	FALSE
mean_EFFECT_05	FALSE
mean_EFFECT_01	FALSE
mean_chisq	FALSE
n_p_sig	FALSE
miss_EFFECT	FALSE
miss_SE	FALSE
miss_PVAL	FALSE
ldsc_ratio	FALSE
ldsc_intercept_beta	FALSE
n_clumped_hits	FALSE
r2_sum1	FALSE
r2_sum2	FALSE
r2_sum3	FALSE
r2_sum4	FALSE

Definitions

General metrics

af_correlation: Correlation coefficient between AF and AF_reference.
inflation_factor (lambda): Genomic inflation factor.
mean_EFFECT: Mean of EFFECT size.
n: Maximum value of reported sample size across all SNPs, \(n\).
n_clumped_hits: Number of clumped hits.
n_snps: Number of SNPs
n_p_sig: Number of SNPs with pvalue below 5e-8.
n_mono: Number of monomorphic (MAF == 1 or MAF == 0) SNPs.
n_ns: Number of SNPs with nonsense values:
- alleles other than A, C, G or T.
- P-values < 0 or > 1.
- negative or infinite standard errors (<= 0 or = Infinity).
- infinite beta estimates or allele frequencies < 0 or > 1.
n_mac: Number of cases where MAC (\(2 \times N \times MAF\)) is less than 6.
is_snpid_unique: true if the combination of ID REF ALT is unique and therefore no duplication in snpid.
n_miss_<*>: Number of NA observations for <*> column.

se_n metrics

n_est: Estimated sample size value, \(\widehat{n}\).
ratio_se_n: \(\texttt{ratio_se_n} = \frac{\sqrt{\widehat{n}}}{\sqrt{n}}\). We expect ratio_se_n to be 1. When it is not 1, it implies that the trait did not have a variance of 1, the reported sample size is wrong, or that the SNP-level effective sample sizes differ markedly from the reported sample size.
mean_diff: \(\texttt{mean_diff} = \sum_{j} \frac{\widehat{\beta_j^{std}} - \beta_j}{\texttt{n_snps}}\), mean difference between the standardised beta, predicted from P-values, and the observed beta. The difference should be very close to zero if trait has a variance of 1.
- \(\widehat{\beta_j^{std}} = \sqrt{\frac{{z}_j^2 / ({z}_j^2 + n -2)}{2 \times {MAF}_j \times (1 - {MAF}_j)}} \times sign({z}_j)\),
- \({z}_j = \frac{\beta_j}{{se}_j}\),
- and \(\beta_j\) is the reported effect size.
ratio_diff: \(\texttt{ratio_diff} = |\frac{\texttt{mean_diff}}{\texttt{mean_diff2}}|\), absolute ratio between the mean of diff and the mean of diff2 (expected difference between the standardised beta predicted from P-values, and the standardised beta derived from the observed beta divided by the predicted SD; NOT reported). The ratio should be close to 1. If different from 1, then implies that the betas are not in a standard deviation scale.
- \(\texttt{mean_diff2} = \sum_{j} \frac{\widehat{\beta_j^{std}} - \beta^{\prime}_j}{\texttt{n_snps}}\)
- \(\beta^{\prime}_j = \frac{\beta_j}{\widehat{\texttt{sd2}}_{y}}\)
sd_y_est1: The standard deviation for the trait inferred from the reported sample size, median standard errors for the SNP-trait assocations and SNP variances.
- \(\widehat{\texttt{sd1}}_{y} = \frac{\sqrt{n} \times median({se}_j)}{C}\),
- \(C = median(\frac{1}{\sqrt{2 \times {MAF}_j \times (1 - {MAF}_j)}})\),
- and \({se}_j\) is the reported standard error.
sd_y_est2: The standard deviation for the trait inferred from the reported sample size, Z statistics for the SNP-trait effects (beta/se) and allele frequency.
- \(\widehat{\texttt{sd2}}_{y} = median(\widehat{sd_j})\),
- \(\widehat{sd_j} = \frac{\beta_j}{\widehat{\beta_j^{std}}}\),

r2 metrics

Sum of variance explained, calculated from the clumped top hits sample.

r2_sum<*>: r2 statistics under various assumptions
- 1: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var1}}}\), \(\texttt{var1} = 1\).
- 2: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var2}}}\), \(\texttt{var2} = {\widehat{\texttt{sd1}}_{y}}^2\),
- 3: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var3}}}\), \(\texttt{var3} = {\widehat{\texttt{sd2}}_{y}}^2\),
- 4: \(r^2 = \sum_j{\frac{F_j}{F_j + n - 2}}\), \(F = \frac{\beta_j^2}{{se}_j^2}\).

LDSC metrics

Metrics from LD regression

ldsc_nsnp_merge_refpanel_ld: Number of remaining SNPs after merging with reference panel LD.
ldsc_nsnp_merge_regression_ld: Number of remaining SNPs after merging with regression SNP LD.
ldsc_observed_scale_h2_{beta,se} Coefficient value and SE for total observed scale h2.
ldsc_intercept_{beta,se}: Coefficient value and SE for intercept. Intercept is expected to be 1.
ldsc_lambda_gc: Lambda GC statistics.
ldsc_mean_chisq: Mean \(\chi^2\) statistics.
ldsc_ratio: \(\frac{\texttt{ldsc_intercept_beta} - 1}{\texttt{ldsc_mean_chisq} - 1}\), the proportion of the inflation in the mean \(\chi^2\) that the LD Score regression intercepts ascribes to causes other than polygenic heritability. The value of ratio should be close to zero, though in practice values of 0.1-0.2 are not uncommon, probably due to sample/reference LD Score mismatch or model misspecification (e.g., low LD variants have slightly higher \(h^2\) per SNP).

Flags

When a metric needs attention, the flag should return TRUE.

af_correlation: abs(af_correlation) < 0.7.
inflation_factor: inflation_factor > 1.2.
n: n (max reported sample size) < 10000.
is_snpid_non_unique: NOT is_snpid_unique.
mean_EFFECT_nonfinite: mean(EFFECT) is NA, NaN, or Inf.
mean_EFFECT_05: abs(mean(EFFECT)) > 0.5.
mean_EFFECT_01: abs(mean(EFFECT)) > 0.1.
mean_chisq: ldsc_mean_chisq > 1.3 or ldsc_mean_chisq < 0.7.
n_p_sig: n_p_sig > 1000.
miss_<*>: n_miss_<*> / n_snps > 0.01.
ldsc_ratio: ldsc_ratio > 0.5
ldsc_intercept_beta: ldsc_intercept_beta > 1.5
n_clumped_hits: n_clumped_hits > 1000
r2_sum<*>: r2_sum<*> > 0.5

Plots

Manhattan plot
- Red line: \(-log_{10}^{5 \times 10^{-8}}\)
- Blue line: \(-log_{10}^{5 \times 10^{-5}}\)
QQ plot
AF plot
P-Z plot
beta_std plot: Scatter plot between \(\widehat{\beta_j^{std}}\) and \(\beta_j\)

Diagnostics

Details

Summary stats

skim_type	skim_variable	n_missing	complete_rate	character.min	character.max	character.empty	character.n_unique	character.whitespace	logical.mean	logical.count	numeric.mean	numeric.sd	numeric.p0	numeric.p25	numeric.p50	numeric.p75	numeric.p100	numeric.hist
character	ID	0	1.0000000	3	58	0	5135032	0	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
character	REF	0	1.0000000	1	3	0	80	0	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
character	ALT	0	1.0000000	1	3	0	80	0	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
logical	N	5135036	0.0000000	NA	NA	NA	NA	NA	NaN	:	NA	NA	NA	NA	NA	NA	NA	NA
numeric	CHROM	0	1.0000000	NA	NA	NA	NA	NA	NA	NA	8.356760e+00	5.629048e+00	1.0000	3.000000e+00	7.000000e+00	1.200000e+01	2.200000e+01	▇▅▃▂▂
numeric	POS	0	1.0000000	NA	NA	NA	NA	NA	NA	NA	7.977423e+07	5.495317e+07	29422.0000	3.532730e+07	7.050636e+07	1.143548e+08	2.492183e+08	▇▇▅▂▁
numeric	EFFECT	0	1.0000000	NA	NA	NA	NA	NA	NA	NA	5.779200e-03	2.870856e-01	-10.4732	-3.580000e-02	7.000000e-04	3.800000e-02	1.122180e+01	▁▁▇▁▁
numeric	SE	0	1.0000000	NA	NA	NA	NA	NA	NA	NA	1.369463e-01	2.496972e-01	0.0233	3.380000e-02	4.740000e-02	1.090000e-01	4.043000e+00	▇▁▁▁▁
numeric	PVAL	0	1.0000000	NA	NA	NA	NA	NA	NA	NA	5.011764e-01	2.879073e-01	0.0000	2.522999e-01	5.018004e-01	7.501999e-01	1.000000e+00	▇▇▇▇▇
numeric	PVAL_ztest	0	1.0000000	NA	NA	NA	NA	NA	NA	NA	5.010161e-01	2.880026e-01	0.0000	2.520853e-01	5.016049e-01	7.501755e-01	1.000000e+00	▇▇▇▇▇
numeric	AF	0	1.0000000	NA	NA	NA	NA	NA	NA	NA	2.781589e-01	2.817943e-01	0.0000	3.560000e-02	1.762000e-01	4.617000e-01	1.000000e+00	▇▃▂▂▁
numeric	AF_reference	377170	0.9265497	NA	NA	NA	NA	NA	NA	NA	2.522964e-01	2.538675e-01	0.0000	3.654150e-02	1.659350e-01	4.039540e-01	1.000000e+00	▇▃▂▁▁

Head and tail

CHROM	POS	ID	REF	ALT	EFFECT	SE	PVAL	PVAL_ztest	AF	AF_reference	N
1	780785	rs2977612	T	A	-0.0270	0.0464	0.5608994	0.5606364	0.8252	0.669329	NA
1	782981	rs6594026	C	T	0.0266	0.0458	0.5608994	0.5613847	0.1534	0.297923	NA
1	783318	rs6686696	A	G	0.0417	0.0717	0.5608000	0.5608429	0.0799	0.183107	NA
1	785050	rs2905062	G	A	-0.0198	0.0340	0.5608994	0.5603290	0.8365	0.626997	NA
1	785989	rs2980300	T	C	-0.0219	0.0377	0.5608994	0.5613066	0.8083	0.626997	NA
1	787121	rs12077234	T	A	0.0347	0.0596	0.5608994	0.5604220	0.1319	NA	NA
1	787399	rs2905055	G	T	-0.0268	0.0461	0.5610002	0.5610080	0.8001	0.646366	NA
1	787685	rs2905054	G	T	-0.0257	0.0441	0.5610997	0.5600505	0.7668	0.622204	NA
1	787844	rs2905053	C	T	-0.0279	0.0480	0.5608994	0.5610720	0.8114	0.651757	NA
1	790758	1_790758_GTA_G	G	GTA	-0.0296	0.0510	0.5608994	0.5616502	0.7799	NA	NA

CHROM	POS	ID	REF	ALT	EFFECT	SE	PVAL	PVAL_ztest	AF	AF_reference	N
22	51163039	rs715584	G	T	-0.0017	0.0301	0.9547000	0.9549607	0.4131	0.4736420	NA
22	51163138	rs715586	C	T	0.0162	0.0361	0.6546995	0.6536095	0.1273	0.0902556	NA
22	51163910	rs192700691	C	T	0.0615	0.1073	0.5665001	0.5665368	0.0304	0.0295527	NA
22	51164109	rs5770995	G	C	-0.0049	0.0283	0.8619000	0.8625376	0.4411	0.5109820	NA
22	51164115	rs5770996	C	T	-0.0046	0.0284	0.8713000	0.8713280	0.4446	0.5147760	NA
22	51164287	rs6009957	T	C	-0.0159	0.0273	0.5615999	0.5602854	0.3052	0.4155350	NA
22	51165664	rs8137951	G	A	-0.0150	0.0266	0.5724994	0.5728155	0.2954	0.4063500	NA
22	51171693	rs756638	G	A	0.0186	0.0387	0.6304999	0.6307865	0.3046	0.3049120	NA
22	51175626	rs3810648	A	G	-0.0346	0.0603	0.5665001	0.5661047	0.0735	0.1084270	NA
22	51178090	rs2285395	G	A	-0.0207	0.0572	0.7171005	0.7174356	0.0481	0.0666933	NA

bcf preview

1   780785  rs2977612   T   A   .   PASS    AF=0.8252   ES:SE:LP:AF:ID  -0.027:0.0464:0.251115:0.8252:rs2977612
1   782981  rs6594026   C   T   .   PASS    AF=0.1534   ES:SE:LP:AF:ID  0.0266:0.0458:0.251115:0.1534:rs6594026
1   783318  rs6686696   A   G   .   PASS    AF=0.0799   ES:SE:LP:AF:ID  0.0417:0.0717:0.251192:0.0799:rs6686696
1   785050  rs2905062   G   A   .   PASS    AF=0.8365   ES:SE:LP:AF:ID  -0.0198:0.034:0.251115:0.8365:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.8083   ES:SE:LP:AF:ID  -0.0219:0.0377:0.251115:0.8083:rs2980300
1   787121  rs12077234  T   A   .   PASS    AF=0.1319   ES:SE:LP:AF:ID  0.0347:0.0596:0.251115:0.1319:rs12077234
1   787399  rs2905055   G   T   .   PASS    AF=0.8001   ES:SE:LP:AF:ID  -0.0268:0.0461:0.251037:0.8001:rs2905055
1   787685  rs2905054   G   T   .   PASS    AF=0.7668   ES:SE:LP:AF:ID  -0.0257:0.0441:0.25096:0.7668:rs2905054
1   787844  rs2905053   C   T   .   PASS    AF=0.8114   ES:SE:LP:AF:ID  -0.0279:0.048:0.251115:0.8114:rs2905053
1   790758  1_790758_GTA_G  G   GTA .   PASS    AF=0.7799   ES:SE:LP:AF:ID  -0.0296:0.051:0.251115:0.7799:1_790758_GTA_G
1   1108637 rs4970421   G   A   .   PASS    AF=0.0713   ES:SE:LP:AF:ID  0.0357:0.0758:0.195384:0.0713:rs4970421
1   1112982 rs6671609   C   T   .   PASS    AF=0.1436   ES:SE:LP:AF:ID  0.0258:0.0601:0.175224:0.1436:rs6671609
1   1115994 rs13376597  G   A   .   PASS    AF=0.1429   ES:SE:LP:AF:ID  0.0249:0.0581:0.174964:0.1429:rs13376597
1   1116231 rs13374146  T   C   .   PASS    AF=0.0678   ES:SE:LP:AF:ID  0.0303:0.0612:0.207048:0.0678:rs13374146
1   1117398 rs12097586  A   G   .   PASS    AF=0.4246   ES:SE:LP:AF:ID  -0.0023:0.0437:0.0189973:0.4246:rs12097586
1   1117486 rs13376670  A   G   .   PASS    AF=0.1481   ES:SE:LP:AF:ID  0.0225:0.0571:0.158578:0.1481:rs13376670
1   1118275 rs61733845  C   T   .   PASS    AF=0.05 ES:SE:LP:AF:ID  0.0268:0.0576:0.192397:0.05:rs61733845
1   1118578 rs111290899 G   A   .   PASS    AF=0.0504   ES:SE:LP:AF:ID  0.0231:0.0589:0.15789:0.0504:rs111290899
1   1119657 rs4560982   G   C   .   PASS    AF=0.4012   ES:SE:LP:AF:ID  -0.0068:0.0392:0.0647447:0.4012:rs4560982
1   1119858 rs1320565   C   T   .   PASS    AF=0.1126   ES:SE:LP:AF:ID  -0.0256:0.0603:0.173277:0.1126:rs1320565
1   1120431 rs1320571   G   A   .   PASS    AF=0.0525   ES:SE:LP:AF:ID  -0.0347:0.0551:0.27638:0.0525:rs1320571
1   1121014 rs3813204   G   A   .   PASS    AF=0.1364   ES:SE:LP:AF:ID  0.0216:0.0571:0.151934:0.1364:rs3813204
1   1121341 rs4297230   C   T   .   PASS    AF=0.1422   ES:SE:LP:AF:ID  0.016:0.0557:0.111427:0.1422:rs4297230
1   1121358 rs80057011  A   C   .   PASS    AF=0.0928   ES:SE:LP:AF:ID  -0.0058:0.0656:0.0315638:0.0928:rs80057011
1   1121480 rs12063663  T   C   .   PASS    AF=0.0923   ES:SE:LP:AF:ID  -0.0005:0.0654:0.00278842:0.0923:rs12063663
1   1121625 rs4081334   C   G   .   PASS    AF=0.1418   ES:SE:LP:AF:ID  0.0181:0.0552:0.128777:0.1418:rs4081334
1   1121657 rs11260548  T   C   .   PASS    AF=0.2302   ES:SE:LP:AF:ID  0.0081:0.0371:0.0818123:0.2302:rs11260548
1   1121715 rs4081333   C   T   .   PASS    AF=0.0882   ES:SE:LP:AF:ID  -0.0057:0.0644:0.0317973:0.0882:rs4081333
1   1121794 rs11260549  G   A   .   PASS    AF=0.1326   ES:SE:LP:AF:ID  0.0199:0.055:0.14436:0.1326:rs11260549
1   1121835 rs57346441  C   CTG .   PASS    AF=0.2304   ES:SE:LP:AF:ID  0.0067:0.0363:0.0691019:0.2304:1_1121835_C_CTG
1   1122024 rs4314833   T   C   .   PASS    AF=0.1279   ES:SE:LP:AF:ID  0.0261:0.0561:0.192397:0.1279:rs4314833
1   1122196 rs4634847   A   G   .   PASS    AF=0.1342   ES:SE:LP:AF:ID  0.0213:0.0547:0.156705:0.1342:rs4634847
1   1122283 rs12064046  T   G   .   PASS    AF=0.0862   ES:SE:LP:AF:ID  -0.0055:0.0639:0.0306773:0.0862:rs12064046
1   1122319 rs7415847   C   T   .   PASS    AF=0.1199   ES:SE:LP:AF:ID  0.0295:0.0599:0.206279:0.1199:rs7415847
1   1122468 rs7545694   T   C   .   PASS    AF=0.2031   ES:SE:LP:AF:ID  0.0091:0.04:0.0863451:0.2031:rs7545694
1   1122516 rs11260551  G   A   .   PASS    AF=0.1274   ES:SE:LP:AF:ID  0.029:0.0559:0.219395:0.1274:rs11260551
1   1122539 rs12063897  A   G   .   PASS    AF=0.0866   ES:SE:LP:AF:ID  -0.005:0.0631:0.0282141:0.0866:rs12063897
1   1122915 rs28595293  A   G   .   PASS    AF=0.2718   ES:SE:LP:AF:ID  -0.0053:0.032:0.0610302:0.2718:rs28595293
1   1122916 rs28460227  A   G   .   PASS    AF=0.0856   ES:SE:LP:AF:ID  -0.0053:0.0632:0.0299787:0.0856:rs28460227
1   1122937 rs28648687  G   A   .   PASS    AF=0.0856   ES:SE:LP:AF:ID  -0.0054:0.0632:0.0306307:0.0856:rs28648687
1   1123106 rs12401472  G   A   .   PASS    AF=0.128    ES:SE:LP:AF:ID  0.0287:0.0555:0.218747:0.128:rs12401472
1   1123434 rs12066716  T   A   .   PASS    AF=0.1323   ES:SE:LP:AF:ID  -0.038:0.0537:0.31894:0.1323:rs12066716
1   1124257 rs10907172  A   G   .   PASS    AF=0.1273   ES:SE:LP:AF:ID  0.0287:0.0552:0.219395:0.1273:rs10907172
1   1124399 rs10907173  C   G   .   PASS    AF=0.1324   ES:SE:LP:AF:ID  0.0242:0.054:0.184622:0.1324:rs10907173
1   1124663 rs6684820   G   A   .   PASS    AF=0.2737   ES:SE:LP:AF:ID  -0.0054:0.0313:0.0638886:0.2737:rs6684820
1   1124819 rs6694487   C   T   .   PASS    AF=0.0867   ES:SE:LP:AF:ID  -0.0055:0.0625:0.031377:0.0867:rs6694487
1   1124891 rs61768485  G   A   .   PASS    AF=0.1266   ES:SE:LP:AF:ID  0.0285:0.055:0.219035:0.1266:rs61768485
1   1125110 rs12124436  T   C   .   PASS    AF=0.1248   ES:SE:LP:AF:ID  0.0289:0.0548:0.223299:0.1248:rs12124436
1   1125220 rs12065129  C   T   .   PASS    AF=0.0864   ES:SE:LP:AF:ID  -0.0053:0.0619:0.0308638:0.0864:rs12065129
1   1125348 rs12029885  T   C   .   PASS    AF=0.1261   ES:SE:LP:AF:ID  0.0263:0.0552:0.198185:0.1261:rs12029885